5HKV

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lincomycin

Structural Biology Knowledgebase: 5HKV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 5HKV

Classification: RIBOSOME

Total Structure Weight: 1364953.88


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 A 277 Staphylococcus aureus Gene Name(s): rplB SAOUHSC_02509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 B 220 Staphylococcus aureus Gene Name(s): rplC SAOUHSC_02512
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 C 207 Staphylococcus aureus Gene Name(s): rplD SAOUHSC_02511
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 D 179 Staphylococcus aureus Gene Name(s): rplE SAOUHSC_02500
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 E 178 Staphylococcus aureus Gene Name(s): rplF SAOUHSC_02496
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 G 145 Staphylococcus aureus Gene Name(s): rplM SAOUHSC_02478
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 H 122 Staphylococcus aureus Gene Name(s): rplN SAOUHSC_02502
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 I 146 Staphylococcus aureus Gene Name(s): rplO SAOUHSC_02492
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 J 144 Staphylococcus aureus Gene Name(s): rplP SAOUHSC_02505
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 K 122 Staphylococcus aureus Gene Name(s): rplQ SAOUHSC_02484
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 L 119 Staphylococcus aureus Gene Name(s): rplR SAOUHSC_02495
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 M 116 Staphylococcus aureus Gene Name(s): rplS SAOUHSC_01211
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 N 118 Staphylococcus aureus Gene Name(s): rplT SAOUHSC_01784
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 O 102 Staphylococcus aureus Gene Name(s): rplU SAOUHSC_01757
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 P 117 Staphylococcus aureus Gene Name(s): rplV SAOUHSC_02507
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 Q 91 Staphylococcus aureus Gene Name(s): rplW SAOUHSC_02510
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 R 105 Staphylococcus aureus Gene Name(s): rplX SAOUHSC_02501
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 S 217 Staphylococcus aureus Gene Name(s): rplY ctc SAUSA300_0479
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 T 94 Staphylococcus aureus Gene Name(s): rpmA SAOUHSC_01755
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 U 62 Staphylococcus aureus Gene Name(s): rpmB SAOUHSC_01191
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 V 69 Staphylococcus aureus Gene Name(s): rpmC SAOUHSC_02504
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 W 59 Staphylococcus aureus Gene Name(s): rpmD SAOUHSC_02493
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 Z 58 Staphylococcus aureus Gene Name(s): rpmF SAOUHSC_01078
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 2 45 Staphylococcus aureus Gene Name(s): rpmH SAOUHSC_03055
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 3 66 Staphylococcus aureus Gene Name(s): rpmI SAOUHSC_01785
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23s ribosomal RNA X 2923 Staphylococcus aureus
5S ribosomal RNA Y 114 Staphylococcus aureus

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3QB
Query on 3QB

X LINCOMYCIN
methyl (5R)-5-[(1R,2R)-2-hydroxy-1-{[(4R)- 1-methyl-4-propyl-L-prolyl]amino}propyl]- 1-thio-beta-L-arabinopyranoside (Synonym)
C18 H34 N2 O6 S
OJMMVQQUTAEWLP-KIDUDLJLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPD
Query on SPD

X, Y SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) (Synonym)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

S, X (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C, I, J, N, R, S, X, Y, Z MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EOH
Query on EOH

C, R, X ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

Y CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

2, 3, A, B, G, K, L, M, O, P, R, S, T, X, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.187
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 280.89 α = 90.00
b = 280.89 β = 90.00
c = 873.52 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-01-14
  • Released Date: 2017-05-03
  • Deposition author(s): Yonath, A., Matzov, D., Eyal, Z., Ben Hamou, R., Zimmerman, E., Rozenberg, H., Bashan, A., Fridman, M.

Revision History

  • 2017-05-10
    Type: Entry authorship | Details: Entry authorship
  • 2017-05-10
    Type: Citation | Details: Citation